The long non-coding RNAs (lncRNA) are transcripts longer than 200 nucleotides and were initially considered as background noises of genomic transcription. Studies of these years showed that lncRNA actually plays active roles in many vital biological processes, such as inactivation of X chromosome, pluripotency maintenance of stems cells, transcriptional regulations and epigenetic regulations. As an important member of lncRNAs, the long intergenic non-coding RNAs (lincRNA) have already been relatively well indentified in the human and mouse genomes. However, although pigs have gone through thousands of years of selection and now are a significant large domestic animal, the contributions of changes of lincRNAs to its domestication are still poorly understood.
To clarify these issues, based on the NCBI EST dataset and the published RNA sequencing dataset, Dr. ZHANG Yaping’s research group (Kunming Institute of Zoology, CAS) conducted a comprehensive genome-wide searching of lincRNAs in pigs and have successfully identified 4515 gene loci (6621 lincRNAs transcripts).
In this study, the expression levels and functional correlations between lincRNAs and their proximal protein coding genes from ten tissues of wild boars were compared. The results showed that the expression level of lincRNA genes is lower than that of protein coding genes, whereas, their expression patterns are correlated and may share cis-regulatory modules.
More importantly, 30 lincRNA genes were found with differential expression profiles between pigs and wild boars. Among them, linc-sscg2561 and its neighboring gene Dnmt3a show differential expression in the frontal cortex, suggesting the possible roles they play in pig domestication by regulating emotional and behavioral plasticity.
This study provides the first comprehensive genome-wide analysis of pig lincRNAs, fulfills our knowledge in the genomes of pigs and the domestication of animals. Main findings have been published on Genome Biology and Evolution (http://gbe.oxfordjournals.org/content/early/2014/06/02/gbe.evu113.short?rss=1). 、